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- PDB-9sq9: Crystal Structure of the MurT/GatD Enzyme Complex from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 9sq9
TitleCrystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes
Components(Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit ...) x 2
KeywordsLIGASE / Peptidoglycan / Amidotransferase / Complex
Function / homology
Function and homology information


lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / transferase activity ...lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / transferase activity / zinc ion binding / ATP binding
Similarity search - Function
: / : / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. ...: / : / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Similarity search - Component
Biological speciesStreptococcus pyogenes MGAS10270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVoelpel, S.V. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Crystal Structure of the MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pyogenes
Authors: Voelpel, S.V. / Stehle, T.
History
DepositionSep 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
C: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
B: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
D: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,89516
Polymers157,2954
Non-polymers1,60012
Water12,737707
1
A: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
C: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2196
Polymers78,6482
Non-polymers5724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-6 kcal/mol
Surface area25340 Å2
MethodPISA
2
B: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
D: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,67610
Polymers78,6482
Non-polymers1,0288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint5 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.280, 101.650, 178.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit ... , 2 types, 4 molecules ABCD

#1: Protein Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT


Mass: 49037.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS10270 (bacteria)
Gene: murT, SAMEA1711581_01631 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8B6J667, lipid II isoglutaminyl synthase (glutamine-hydrolysing)
#2: Protein Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase glutaminase subunit


Mass: 29610.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS10270 (bacteria)
Gene: gatD, E0F67_01185 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5S4TG60, lipid II isoglutaminyl synthase (glutamine-hydrolysing), glutaminase

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Non-polymers , 5 types, 719 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24 % (w/v) PEG 3,350 200 mM tri-ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.05→44.15 Å / Num. obs: 91872 / % possible obs: 90.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 35.96 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1435 / Rpim(I) all: 0.0504 / Rrim(I) all: 0.1527 / Net I/σ(I): 9
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.747 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 9310 / CC1/2: 0.557 / CC star: 0.846 / Rpim(I) all: 0.6366 / % possible all: 93.08

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→44.14 Å / SU ML: 0.2426 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2181 1837 2 %
Rwork0.1743 90001 -
obs0.1752 91838 90.58 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.81 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10039 0 100 707 10846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010910377
X-RAY DIFFRACTIONf_angle_d1.215914100
X-RAY DIFFRACTIONf_chiral_restr0.07481596
X-RAY DIFFRACTIONf_plane_restr0.00631830
X-RAY DIFFRACTIONf_dihedral_angle_d13.7076118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.3271440.29057045X-RAY DIFFRACTION93.24
2.11-2.170.32271430.26267021X-RAY DIFFRACTION92.73
2.17-2.240.34251420.24676963X-RAY DIFFRACTION92.25
2.24-2.320.26031410.22776881X-RAY DIFFRACTION90.96
2.32-2.410.2921430.2187021X-RAY DIFFRACTION93.06
2.41-2.520.28781440.20577027X-RAY DIFFRACTION92.42
2.52-2.650.22111410.19466943X-RAY DIFFRACTION91.58
2.65-2.820.22651420.19016923X-RAY DIFFRACTION90.88
2.82-3.040.27151400.1856875X-RAY DIFFRACTION90.17
3.04-3.340.25381380.17736758X-RAY DIFFRACTION88.31
3.34-3.830.1921400.15576885X-RAY DIFFRACTION89.43
3.83-4.820.1421400.12746846X-RAY DIFFRACTION88.15
4.82-44.140.18141390.15236813X-RAY DIFFRACTION84.93

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